“We have contacted (Microsoft) through official channels about concerns about the similarities between Bing and Kayak,” Robert Birge, Kayak’s chief marketing officer, told Wired in June 2009. “From the look and feel of their travel product, they seem to agree with our approach to the market.”

So I thought it was a little strange when I got an e-mail from Microsoft PR this morning saying that Bing Travel will soon integrate Kayak’s flight-search services. Was this the result of some years-long, behind-the-scenes legal negotiation? Or something?

I decided to check in with Birge. The answer, it turns out, is no.

Nope! In fact, Birge hardly even remembered that little exchange.

“If we did have discussions (with Microsoft), those discussions were behind closed doors and agreed as level-headed businesspeople,” he told me. Today’s partnership “has to do with the strategy that Bing is taking as a general search engine with more specific search-engine verticals … from third parties.”

I also double-checked with a Microsoft spokesperson, who sent me the following response via e-mail:

With regards to your question about Kayak’s past claims being a result (or driving force) of this partnership, the answer is no. Bing is partnering with Kayak to help customers make faster, more informed travel decisions. Bing Travel tools, together with Kayak’s comprehensive travel search results, will allow travelers to easily and quickly find the best airfare on the Web.

So there are the talking points. The business deal, of course, was financial — though the companies aren’t disclosing specifics. And Birge, from the sound of it, is excited to be working closely with Bing and its “unique approach to the user interface.” (Which, I’d just like to point out again, Birge two years ago said was eerily similar to Kayak’s. To be fair, Microsoft has changed the flight-results design a bit since then. Here’s a full comparison.)

Microsoft gets access to all of Kayak’s travel-search services, and will begin by sucking-in Kayak’s flight data — replacing some of Bing Travel’s under-the-hood technology. Microsoft is still providing its own airfare predictor and instant flight search results.

Kayak is also gaining access to Microsoft technology. Right now, the Norwalk, Conn.-based company is looking at using Bing Maps, Birge said.

Kayak, like Bing Travel, uses flight data from ITA Software — and a number of other sources — in its services. Why would Microsoft insert a middleman like Kayak when it’s already sucking in much of the same data?

It’s not so simple, Birge said. ITA Software provides tons of data, but companies like Kayak build fine-tuning algorithms over that data to make, for instance, their airfare predictions more accurate. Microsoft apparently liked Kayak’s way of doing things better than its own.

And yes, ITA Software is the flight-data giant that Google is trying to acquire for $700 million. The deal, however, has gained the interest of U.S. antitrust authorities, and Google competitors — including Microsoft and Kayak — have asked the Department of Justice to block the deal.

“We’re very concerned about Google being able to choke off access to that product,” Birge said.